depristo
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6ffcaa0afe
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Can run R scripts on the command line
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3750 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-09 00:13:18 +00:00 |
rpoplin
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64fc76e4bf
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Added an option to AnalyzeCovariates to set the max value of the histograms to make them easier to directly compare.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2753 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-31 23:13:57 +00:00 |
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rpoplin
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cea544871d
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Fixed an issue with recalibrating original quality scores above Q40. There is a new option -maxQ which sets the maximum quality score possible for when a RecalDatum tries to compute its quality score from the mismatch rate. The same option was added to AnalyzeCovariates to help with plotting q scores above Q40. Added an integration test which makes use of this new -maxQ option.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2534 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-07 13:50:30 +00:00 |
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rpoplin
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562db45fa5
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Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2451 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-28 20:19:37 +00:00 |
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rpoplin
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088363ce42
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Added entropy calculation to histogram of quality scores
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2316 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-10 21:57:35 +00:00 |
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rpoplin
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855face681
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Histogram of covariate values now goes from 0 to max value which makes it look nicer in most cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2259 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-04 14:44:03 +00:00 |
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rpoplin
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985daec76e
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Fixed problem with integer overflow in R scripts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2258 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-04 14:24:49 +00:00 |
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rpoplin
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2508deca37
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Prevented data points with fewer than N observations from going off the edge of the plots
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2257 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-04 13:55:43 +00:00 |
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rpoplin
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46f3d3e39b
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Added comments to AnalyzeCovariates and R scripts. R script prevents residuals from going off the edge of the plot. Added skeleton code to the recalibration walkers showing how we plan to handle SOLID reference inserting behavior.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2233 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 23:15:52 +00:00 |
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rpoplin
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67179e2412
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Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 16:47:35 +00:00 |